Comparative analysis of chromosome interaction networks in 12 human cell types using Hi-C.

Abstract

Chromosome-scale three-dimensional interaction patterns within the nucleus represent a critical layer of higher-order genome organization. However, systematic comparative analyses of chromosome-scale interchromosomal interaction patterns across diverse cell types remain limited. In this study, we analyzed high-quality Hi-C datasets from 12 human cell types in the 4D Nucleome database, including pluripotent cells, hematopoietic lineage cells, tissue-specific cells, and cancer cells. To reduce scale bias in interchromosomal interaction analysis, we applied and validated a computational strategy based on chromosome length normalization. We further performed aggregation analysis at the cytogenetic G-banding level to quantitatively characterize chromosome spatial organization at the macroscopic scale. Our results showed that chromosome-scale organization in human cells follows a pattern of "conserved backbone with local modifications". A core spatial backbone composed of small chromosomes, including Chr16, Chr17, Chr19, and Chr20, was highly conserved across all examined cell types, whereas large chromosomes such as Chr2, Chr3, and Chr4 consistently ranked lower in interaction frequency. These findings support the large-scale stability of the chromosome territory model. Lineage analysis further showed that during hematopoietic differentiation, the modularity index of chromosome interaction networks increased significantly with functional specialization from 0.0417 to 0.0554, with P<0.0001 by Mann-Whitney U test, whereas tissue-specific cells maintained a stable structural state. In cancer cells, although the core backbone was preserved, abnormal interchromosomal interaction hotspots associated with structural variation were observed, such as Chr12-Chr21 in K562 and Chr8-Chr16 in HCT116. Overall, we systematically delineated chromosome-scale interaction patterns across distinct cellular lineages, providing new insights into the spatial organization principles of chromosomes in the nucleus and a reference framework for future studies linking three-dimensional genome architecture with structural genomic variation.